by Tamara Scully

Onion production occurs in volume in select regions throughout the U.S. The Midwest, the Rockies, the Northeast, the Pacific Northwest, all of California, Southeastern states and the Southwest regions each have substantial production of onions.

But storage onions are often plagued with rot. Economic losses due to bacterial pathogens in onions – primarily rot – amount to more than $50 million each year, according to Washington State University.

The “Stop the Rot” study is a collaboration of researchers around the country dedicated to preventing, treating and understanding onion rots. The USDA-NIFA project, spearheaded by WSU and funded in 2019, “takes a systems approach encompassing the pathogen, host, environment, economics and stakeholder priorities to address the need to manage onion bacterial diseases far more effectively.”

The researchers plan to identify and genomically examine the bacterial pathogens which cause rot across all of the important onion-growing regions, with the intent to develop methods to rapidly detect pathogens as well as to breed resistant cultivars. The second objective is to understand how farm management – fertility, irrigation, harvest and storage – can impact bacterial rot. The project is scheduled to be completed in 2023.

“One of the problems is that there may not be any symptoms in the bulbs when they are harvested from the field and go into the packing shed and into storage. The development of those symptoms might happen in storage,” WSU Plant Pathologist Lindsey du Toit said.

Diagnosing Bacterial Diseases

Symptoms of bacterial rot are similar to those often caused by fungi or by abiotic concerns, such as weather issues or mechanical or chemical damage. And numerous bacterial pathogens can infect onions. These factors make the proper identification of any rot difficult.

“They can result in symptoms that look very similar to bacterial diseases,” du Toit said of fungal pathogens and abiotic concerns. “So it’s really important for growers to understand accurately what’s causing the problem.”

Another issue arises when common names for onion diseases, such as “neck rot,” are used. True onion neck rot is a fungal disease, caused by Botrytis spp., and not by bacteria. But rot in onion necks is also a primary sign of bacterial infection. Rots caused by fungal pathogens are managed differently than bacterial rots, so misidentification is problematic.

In the laboratory, bacterial pathogens are injected into onion bulbs, which are then kept at temperatures conducive that particular pathogen’s growth requirements. Some bacterial pathogens, such as Pantoea agglomerans and Burkholderia gladioli v. allicola, rapidly colonize and destroy tissue. Others, including Enterobacter cloacae and Pseudomonas viridiflava, are less aggressive and progress slowly.

Depending on growing region, different bacterial pathogens are prominent. Some pathogens prefer the humid and cool growing conditions during the onion season in Georgia; others thrive in the hot, wet weather often experienced during the onion growing season in regions of the Northwest.

When onions are in the field, bacteria enter from the leaves and progress down the neck and into the bulb. Lesions are seen as the bacteria colonize the leaf tissue. As the pathogen colonizes the neck, it becomes mushy. From there, the bacteria invade the bulb.

Fungal pathogens causing onion rots also cause soft rot in the neck. But the fungal diseases cause a drier type of rot in the bulb, and black sclerotia or fluffy molds are seen on the bulb. In contrast, bacterial rots are wet and slimy, smell awful and cause the bulb to look water-soaked. The bulb can appear brown, pinkish or blue-green, and squeezing the mushy tissue of the neck will often cause liquid to spurt out.

Secondary bacterial infections begin in the bottom of the onion bulb. This would occur after a primary fungal pathogen causes disease in the onion bulb.

Management of Bacterial Disease

Many of the pathogenic bacteria causing onion rot are found naturally in soils. Weeds – often asymptomatic – can also harbor the pathogens. Moisture levels, temperatures and injury are other predisposing factors. Incomplete curing or improper curing methods can contribute to bacterial growth in storage. Seeds can be the initial inoculum source for some of the bacterial rot pathogens, and along with transplants should come from clean sources.

Bacterial pathogens in onions can be spread via splashing water. They thrive in moist conditions. Irrigation can contribute to bacterial rots, and timing and amount of irrigation is critical. Overhead irrigation is conducive to bacterial rot development.

Rapid termination of irrigation at the end of the growing season can be a contributing factor. Studies conducted in 2020 show that ending irrigation after the final leaf emergence, with 5% – 10% tops down, resulted in less storage rot than when irrigated for two additional weeks, when 93% tops down occurred. Researchers continued the study in 2021 and will further it in 2022 as part of the “Stop the Rot” research.

Fertility also contributes to bacterial rot prevalence. The amount of fertilizer and when it’s applied, as well as when it is stopped, can impact bacterial rot development, du Toit said.

Under cutting and topping onions, field drying and the curing and storage environments are other opportunities for bacterial rots to spread. Storm damage or damage from thrips or other pests create wounds which allow bacterial pathogens easy access. If onions are not thoroughly dried prior to storage, bacterial rots can thrive. However, drying with heat can exacerbate problems, as many of the bacterial rot pathogens thrive in hot temperatures. Drying with air can decrease loss.

Some Common Bacterial Rots

A new species of bacteria, Pseudomonas alliiovorans, was recently discovered via genetic testing by University of Georgia vegetable disease specialist Bhabesh Dutta as part of the “Stop the Rot” research. It causes symptoms relatively identical to the streak and bulb rot caused by P. viridiflava.

Pantoea spp. cause center rot in onion, which enters via the foliage and causes tissue desiccation and wilting in the leaves, can be seed-borne, and is believed to be insect vectored by thrips. These pathogens can be hosted by weed species. There is no genetically resistant onion cultivar currently. In the bulb, scales are infected individually while others can remain healthy.

Burkholderia is the causal agent of sour skin in onions. Leaves wilt and die back and are watery. A slimy ring in the bulb occurs as the pathogen invades. The pathogen is found in soil and is distributed via water and prefers warm temperatures. Bulbs show a tan-colored ring when cut open and smell putrid.

Copper bactericides can be used if conditions favor development of bacterial rot pathogens.

Look for more research results as “Stop the Rot” gathers data, conducts trials and publishes information to help onion growers limit losses from bacterial rots.